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- EMDB-62359: Terminator and trunk structure of Escherichia phage Mu -

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Basic information

Entry
Database: EMDB / ID: EMD-62359
TitleTerminator and trunk structure of Escherichia phage Mu
Map data
Sample
  • Complex: Escherichia phage Mu
    • Protein or peptide: Tail sheath protein
    • Protein or peptide: Probable tail terminator protein
    • Protein or peptide: Tail tube protein
Keywordssheath / tube / phage / VIRAL PROTEIN
Function / homology
Function and homology information


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / virus tail, tube / viral tail assembly / virus tail / host cell cytoplasm
Similarity search - Function
Bacteriophage Mu, Gp37 / Bacteriophage Mu, Gp37 / Bacteriophage Mu, GpM, tail tube / Phage tail tube protein / Tail sheath protein / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Tail sheath protein / Tail tube protein / Probable tail terminator protein
Similarity search - Component
Biological speciesEscherichia phage Mu (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhou JQ / Liu HR
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: J Virol / Year: 2025
Title: structures of the contractile nanomachine myophage Mu in both its extended and contracted states.
Authors: Junquan Zhou / Liwen Wang / Hao Xiao / Wenyuan Chen / Zhonghua Liu / Jingdong Song / Jing Zheng / Hongrong Liu /
Abstract: Myophage Mu is a representative of contractile nanomachines with a simple tail baseplate. It has the capacity to infect a range of intestinal bacteria and has extensive applications in genetic ...Myophage Mu is a representative of contractile nanomachines with a simple tail baseplate. It has the capacity to infect a range of intestinal bacteria and has extensive applications in genetic engineering research. Nevertheless, a comprehensive understanding of the entire structure and contractile mechanisms of Mu remains elusive. Using cryo-electron microscopy (cryo-EM), we resolved the asymmetric structures of Mu in both its extended and contracted states, the latter of which lacked the tail baseplate, at near-atomic resolutions. We built the atomic models for the extended Mu, encompassing the head, the connector complex, the tail, and the simple baseplate. It is noteworthy that we identified the position and structure of the tail tube initiator protein gp43 (referred to as the DNA circularization protein). The protein gp43 plays a crucial role not only in the baseplate assembly and DNA circularization but also in stabilizing the wedge-hub connection and mediating tail contraction. Except for the baseplate structure, the structural comparison of Mu in its extended and contracted states revealed that only the tail sheath protein gp39 and the C-terminus of the tail terminator protein gp37 undergo notable conformational changes to accommodate the tail contraction, whereas the remaining protein components remained unchanged. Our structures exhibited conserved properties among the majority of myophages, thereby providing valuable insights into the contraction mechanisms across myophages and contractile injection systems (CISs).
IMPORTANCE: Despite extensive study, the asymmetric structures of phage Mu, a highly effective transposable myophage, remain unknown. In this study, we present the high-resolution structures of Mu in ...IMPORTANCE: Despite extensive study, the asymmetric structures of phage Mu, a highly effective transposable myophage, remain unknown. In this study, we present the high-resolution structures of Mu in both its extended and contracted states. The comparison of the two structures allows for the illustration of detailed conformational changes of the head-to-tail complex during the process of tail contraction. The contraction mechanism of Mu is highly conserved and widely adapted to all contractile nanomachines that share common structural features with Mu.
History
DepositionNov 11, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62359.png

Downloads & links

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Map

FileDownload / File: emd_62359.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 440 pix.
= 598.4 Å		1.36 Å/pix.
x 440 pix.
= 598.4 Å		1.36 Å/pix.
x 440 pix.
= 598.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.0
Minimum - Maximum-18.323729 - 37.904068000000002
Average (Standard dev.)-0.009918608 (±1.7996042)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 598.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62359_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62359_half_map_2.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage Mu

EntireName: Escherichia phage Mu (virus)
Components
  • Complex: Escherichia phage Mu
    • Protein or peptide: Tail sheath protein
    • Protein or peptide: Probable tail terminator protein
    • Protein or peptide: Tail tube protein

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Supramolecule #1: Escherichia phage Mu

SupramoleculeName: Escherichia phage Mu / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage Mu (virus)

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Macromolecule #1: Tail sheath protein

MacromoleculeName: Tail sheath protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 53.132508 KDa
SequenceString: MSDISFNAIP SDVRVPLTYI EFDNSNAVSG TPAPRQRVLM FGQSGSKASA APNVPVRIRS GSQASAAFGQ GSMLALMADA FLNANRVAE LWCIPQGNGT GNAAVGEISL SGTAGENGSL VTYIAGQRLA VSVAAGATGA ALADLLVARI KGQPDLPVTA E VRADSGDD ...String:
MSDISFNAIP SDVRVPLTYI EFDNSNAVSG TPAPRQRVLM FGQSGSKASA APNVPVRIRS GSQASAAFGQ GSMLALMADA FLNANRVAE LWCIPQGNGT GNAAVGEISL SGTAGENGSL VTYIAGQRLA VSVAAGATGA ALADLLVARI KGQPDLPVTA E VRADSGDD DTHADVVLSA KFTGALSAVD VRWNYYAGET TPYGIITAFK AASGKNGNPD ISASIAGMGD LQYKYIVMPY TD EPNLNLL RTELQERWGP VNQADGFAVT VLSGTYGDIS TFGVSRNDHL ISCMGIAGAP EPSYLYAATL CAVASQALSI DPA RPLQTL TLPGRMPPAV GDRFTWSERN ALLFDGISTF NVNDGGEMQI ERMITMYRTN KYGDSDPSYL NVNTIATLSY LRYS LRTRI TQKFPNYKLA SDGTRFATGQ AVVTPSVIKT ELLALFEEWE NAGLVEDFDT FKEELYVARN KDDKDRLDVL CGPNL INQF RIFAAQVQFI L

UniProtKB: Tail sheath protein

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Macromolecule #2: Probable tail terminator protein

MacromoleculeName: Probable tail terminator protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 20.576053 KDa
SequenceString:
MLEETEAALL ARVRELFGAT LRQVEPLTGT WTNEDVHRLF LAPPSVFLAW MGCGEGRTRR EVESRWAFFV VAELLNGEPV NRPGIYQIV ERLIAGVNGQ TFGPTTGMRL TQVRNLCDDN RINAGVVLYG VLFSGTTPLP SVVDLDSLDD YERHWQTWKF P DETPEFAA HINVNQEKDH DAEN

UniProtKB: Probable tail terminator protein

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Macromolecule #3: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 12.84047 KDa
SequenceString:
MAGNQRQGVA FIRVNGMELE SMEGASFTPS GITREEVTGS RVYGWKGKPR AAKVECKIPG GGPIGLDEII DWENITVEFQ ADTGETWML ANAWQADEPK NDGGEISLVL MAKQSKRIA

UniProtKB: Tail tube protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55035
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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